Hi Doug,

Thanks for the response.

Regarding #1, I am still confused. if the ROI boundaries computed in native space are mapped to fsaverage/mni305 space, doesn't that mean the actual computing of the averages is done in fsaverage/mni305 space? Why would mapping to fsaverage/mni305 space be necessary in the ROI analysis if the averages are computed in native space?

Regarding #2, I tried that already and got the error "must specify an output table file" (I used the exact same command, just swapping out -slabel for -seg.) Also, this analysis is purely done in mni305/fsaverage space because it is using the concatenated file, correct? If I want to do it in native space, would I use label to label (as written below) and then funcroi? Do you think it would make a difference either way?

mri_label2label --srclabel ${SUBJECTS_DIR}/fsaverage/label/mylabel.label --src subject fsaverage --trglabel ${SUBJECTS_DIR}/subject/label/mylabel.label --trgsubject subject -regmethod surface --hemi lh

Thanks, Emily

On Mar 28, 2014, at 11:15 AM, Douglas N Greve wrote:

On 03/28/2014 08:51 AM, Emily Boeke wrote:

...

Hi Freesurfers,

I have some questions about ROI analyses.

1. I use the mni305 and fsaverage flags during preprocessing. Does this mean that when I run funcroi-config, funcroi-sess, etc, the analysis is being done for each subject in mni305 space, as opposed to native space? Meaning, If I specify -seg aseg.mgz 18 in funcroi-config, the analysis will not be done using the left amygdala from that individual's aseg, but instead will be done in mni305 space with the fsaverage left amygdala ROI?

No, it is done in native space. The voxelwise analysis is done in fsaverage/mni305 space, but the ROI boundaries used to compute the ROI averages are computed in native space and mapped to fsaverage/mni305 space.

...

2. I sometimes want to use labels I've created on fsaverage from averaged group activation to do ROI analyses. If the ROI is in the volume, I convert the label to a mask and run:

mri_segstats --i cespct.nii.gz --seg mymask.mgz --id 1 --avgwf ces.mymask.dat

In the appropriate contrast folder. What should I do if I want to do the same thing, but with a surface label (in a lh or rh surface analysis, not an mni305 analysis)?

You can still use mri_segstats, just spec --slabel instead of seg doug

...

Thanks!

Emily

-- Douglas N. Greve, Ph.D. MGH-NMR Center greve@nmr.mgh.harvard.edu Phone Number: 617-724-2358 Fax: 617-726-7422

Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting FileDrop: https://gate.nmr.mgh.harvard.edu/filedrop2 www.nmr.mgh.harvard.edu/facility/filedrop/index.html Outgoing: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/

I tried to do surfer reconstruction (version 5.3) collected in SIEMENS 7T, with error: imgreg_4dfp /opt/freesurfer-530/average/711-2C_as_mni_average_305 /opt/freesurfer-530/average/711-2B_as_mni_average_305_mask talsrcimg_g11 none talsrcimg_to_711-2C_as_mni_average_305_t4 1283' failed! status=254. This seems happened for many others. However, the reconstruction worked fine as using data collected from 3T, which means the freesurfer was installed correct, and environment settings are correct as well. Also, the reconstruction on the 7T data can go through using additional parameter: -use-mritotal. My question is how the -use-mritotal parameter would affect final surface? Thanks for providing your input on this. Xiaomin Yue

Hi Joe, Thanks for your response. For the future reference, it also needs the parameter -notal-check, otherwise it will fail again. Although the reconstruction was completed surprisingly without error, a significant amount of cortex in the top of the brain was cut off in the brain.mgz file. It needs to be rerun after correcting that error(s). Xiaomin

Date: Tue, 1 Apr 2014 19:52:53 -0400 From: jonp@nmr.mgh.harvard.edu To: freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] recon all with 7T data

hi Xiaomin,

7T data can sometimes cause Talairach failures with the standard registration tools due to the strong bias fields. the Talairach transformation is used for identifying seed points, and the -use-mritotal flag just specifies that the MINC software will be used for the Talairach'ing.

see this page for more info: http://freesurfer.net/fswiki/talairach?highlight=%28use%5C-mritotal%29

-jon

On Fri, 28 Mar 2014, Xiaomin Yue wrote:

...

I tried to do surfer reconstruction (version 5.3) collected in SIEMENS 7T, with error: imgreg_4dfp /opt/freesurfer-530/average/711-2C_as_mni_average_305 /opt/freesurfer-530/average/711-2B_as_mni_average_305_mask talsrcimg_g11 none talsrcimg_to_711-2C_as_mni_average_305_t4 1283' failed! status=254. This seems happened for many others. However, the reconstruction worked fine as using data collected from 3T, which means the freesurfer was installed correct, and environment settings are correct as well. Also, the reconstruction on the 7T data can go through using additional parameter: -use-mritotal. My question is how the -use-mritotal parameter would affect final surface? Thanks for providing your input on this. Xiaomin Yue

---

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Hi Falk, Thanks for this valuable information. For sure, I will try it out, and let you know how it goes. Xiaomin

From: falk.luese@gmx.net To: freesurfer@nmr.mgh.harvard.edu Date: Thu, 3 Apr 2014 00:32:23 +0000 Subject: Re: [Freesurfer] recon all with 7T data

Hi Xiaomin, you could also try to follow the first few steps of the HiresRecon (http://surfer.nmr.mgh.harvard.edu/fswiki/HiResRecon). The parameters of the inhomogeneity correction are optimized for 7T data which should help in reducing errors due to strong bias fields. Best,Falk Von: Xiaomin Yue Gesendet: ‎Mittwoch‎, ‎2‎. ‎April‎ ‎2014 ‎15‎:‎23 An: Freesurfer support list Hi Joe, Thanks for your response. For the future reference, it also needs the parameter -notal-check, otherwise it will fail again. Although the reconstruction was completed surprisingly without error, a significant amount of cortex in the top of the brain was cut off in the brain.mgz file. It needs to be rerun after correcting that error(s). Xiaomin

Date: Tue, 1 Apr 2014 19:52:53 -0400 From: jonp@nmr.mgh.harvard.edu To: freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] recon all with 7T data

hi Xiaomin,

7T data can sometimes cause Talairach failures with the standard registration tools due to the strong bias fields. the Talairach transformation is used for identifying seed points, and the -use-mritotal flag just specifies that the MINC software will be used for the Talairach'ing.

see this page for more info: http://freesurfer.net/fswiki/talairach?highlight=%28use%5C-mritotal%29

-jon

On Fri, 28 Mar 2014, Xiaomin Yue wrote:

...

I tried to do surfer reconstruction (version 5.3) collected in SIEMENS 7T, with error: imgreg_4dfp /opt/freesurfer-530/average/711-2C_as_mni_average_305 /opt/freesurfer-530/average/711-2B_as_mni_average_305_mask talsrcimg_g11 none talsrcimg_to_711-2C_as_mni_average_305_t4 1283' failed! status=254. This seems happened for many others. However, the reconstruction worked fine as using data collected from 3T, which means the freesurfer was installed correct, and environment settings are correct as well. Also, the reconstruction on the 7T data can go through using additional parameter: -use-mritotal. My question is how the -use-mritotal parameter would affect final surface? Thanks for providing your input on this. Xiaomin Yue

---

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The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.

_______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.

Use --id 1 or --excludeid 0 with mri_segstats. 3rd question answered below.

On 04/01/2014 10:42 AM, Emily Boeke wrote:

Hi Doug,

I am able to run mri_segstats with slabel below, but it is finding two segmentations in my label and producing a column for each. one is associated with an ID of 0 and one is associated with an ID of 1. I assume that I want the 2nd column (the ID of 1). What is the command doing? Is it creating one segmentation out of my label and one out of the rest of the cortical surface?

Also, could you please address the 3rd question from the email below? Thanks so much!

Best, Emily On Mar 28, 2014, at 12:37 PM, Douglas N Greve wrote:

...

On 03/28/2014 12:04 PM, Emily Boeke wrote:

...

Hi Doug,

Thanks for the response.

Regarding #1, I am still confused. if the ROI boundaries computed in native space are mapped to fsaverage/mni305 space, doesn't that mean the actual computing of the averages is done in fsaverage/mni305 space? Why would mapping to fsaverage/mni305 space be necessary in the ROI analysis if the averages are computed in native space

What I mean is that the ROI used is that of the native subject, not fsaverage. If you were to map the hippocampus to fsaverage and overlay it with the hippo of fsaverage you would see that they are different. FSFAST resamples the time series data into fsaverage/mni space and computes all the stats there, so the ROI boundaries need to be transferred to that space.

...

Regarding #2, I tried that already and got the error "must specify an output table file" (I used the exact same command, just swapping out -slabel for -seg.)

You can't swap them out. Read the docs for it.

...

Also, this analysis is purely done in mni305/fsaverage space because it is using the concatenated file, correct? If I want to do it in native space, would I use label to label (as written below) and then funcroi? Do you think it would make a difference either way?

I think you can do it in native space if you specify native when you run mkanalysis-sess doug

...

...

mri_label2label --srclabel ${SUBJECTS_DIR}/fsaverage/label/mylabel.label --src subject fsaverage --trglabel ${SUBJECTS_DIR}/subject/label/mylabel.label --trgsubject subject -regmethod surface --hemi lh

Thanks, Emily

On Mar 28, 2014, at 11:15 AM, Douglas N Greve wrote:

...

On 03/28/2014 08:51 AM, Emily Boeke wrote:

...

Hi Freesurfers,

I have some questions about ROI analyses.

1. I use the mni305 and fsaverage flags during preprocessing. Does this mean that when I run funcroi-config, funcroi-sess, etc, the analysis is being done for each subject in mni305 space, as opposed to native space? Meaning, If I specify -seg aseg.mgz 18 in funcroi-config, the analysis will not be done using the left amygdala from that individual's aseg, but instead will be done in mni305 space with the fsaverage left amygdala ROI?

No, it is done in native space. The voxelwise analysis is done in fsaverage/mni305 space, but the ROI boundaries used to compute the ROI averages are computed in native space and mapped to fsaverage/mni305 space.

...

2. I sometimes want to use labels I've created on fsaverage from averaged group activation to do ROI analyses. If the ROI is in the volume, I convert the label to a mask and run:

mri_segstats --i cespct.nii.gz --seg mymask.mgz --id 1 --avgwf ces.mymask.dat

In the appropriate contrast folder. What should I do if I want to do the same thing, but with a surface label (in a lh or rh surface analysis, not an mni305 analysis)?

You can still use mri_segstats, just spec --slabel instead of seg doug

...

Thanks!

Emily

-- Douglas N. Greve, Ph.D. MGH-NMR Center greve@nmr.mgh.harvard.edu Phone Number: 617-724-2358 Fax: 617-726-7422

Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting FileDrop: https://gate.nmr.mgh.harvard.edu/filedrop2 www.nmr.mgh.harvard.edu/facility/filedrop/index.html Outgoing: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/

-- Douglas N. Greve, Ph.D. MGH-NMR Center greve@nmr.mgh.harvard.edu Phone Number: 617-724-2358 Fax: 617-726-7422

Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting FileDrop: https://gate.nmr.mgh.harvard.edu/filedrop2 www.nmr.mgh.harvard.edu/facility/filedrop/index.html Outgoing: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/